🔀 Merge: solve merge conflicts and merge updated main into config-generator branch

sayalaruano · sayalaruano · commit fd424b52fc37 · 2024-12-11T17:39:21.000+01:00
diff --git a/.github/workflows/cdci.yml b/.github/workflows/cdci.yml
@@ -0,0 +1,33 @@
+name: Python package
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  release:
+    types: [published]
+    
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip' # caching pip dependencies
+          cache-dependency-path: '**/pyproject.toml'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install pytest
+          pip install -e .
+      - name: Run tests
+        run: python -m pytest tests
+  
diff --git a/README.md b/README.md
@@ -34,16 +34,46 @@ Also, the class diagram for the project is presented below to illustrate the arc
 </p>
 
 ## Installation
-......
+
+You can install the package for development from this repository by running the following command:
+
+```bash
+pip install -e path/to/vuegen # specify location 
+pip install -e . # in case you pwd is in the vuegen directory
+```
+
+### Quatro installation
+
+Install quatro with vueguen if you don't have it globally installed.
+
+```bash
+pip install -e ".[quarto]" # specify location
+```
+
+if you use conda a conda environement you can install quatro from the conda-forge channel 
+in case it did not work.
+
+```bash
+conda install -c conda-forge quarto
+```
+
+Test your quarto installation by running the following command:
+
+```bash
+quarto check
+```
+
 
 ## Execution
-``` shell
-python vuegen/main.py --config report_config_micw2graph.yaml --report_type streamlit 
+
+```bash
+python vuegen/main.py --config example_data/MicW2Graph/report_config_micw2graph.yaml --report_type streamlit
 ```
+
 The current report types are streamlit, html, pdf, docx, odt, revealjs, pptx, and jupyter.
 
 ## Contact
 If you have comments or suggestions about this project, you can [open an issue][issues] in this repository.
 
 [issues]: https://github.com/Multiomics-Analytics-Group/vuegen/issues/new
-[streamlit]: https://streamlit.io/ 
+[streamlit]: https://streamlit.io/ 
diff --git a/example_data/MicW2Graph/report_config_micw2graph.yaml b/example_data/MicW2Graph/report_config_micw2graph.yaml
@@ -9,8 +9,8 @@ report:
     infer potential interactions among microorganisms through microbial association networks (MANs). MicW2Graph enables the 
     investigation of research questions related to WWT, focusing on aspects such as microbial connections, community memberships, 
     and potential ecological functions.
-  graphical_abstract: /Users/asaru/Documents/DTU/MoNA/vuegen/example_data/MicW2Graph/Methods_MicW2Graph.png
-  logo: /Users/asaru/Documents/DTU/MoNA/vuegen/docs/images/vuegen_logo.png
+  graphical_abstract: example_data/MicW2Graph/Methods_MicW2Graph.png
+  logo: docs/images/vuegen_logo.png
 sections:
   - title: Exploratory Data Analysis
     subsections:
@@ -25,34 +25,34 @@ sections:
           - title: Multiline plot (altair)
             component_type: plot
             plot_type: altair
-            file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/example_data/MicW2Graph/1_Exploratory_Data_Analysis/1_Abundance_data/2_multilineplot_altair.json
+            file_path: example_data/MicW2Graph/1_Exploratory_Data_Analysis/1_Abundance_data/2_multilineplot_altair.json
           - title: Abundance data for all studies (csv)
             component_type: dataframe
             file_path: https://raw.githubusercontent.com/sayalaruano/report_generator_st_cloud_test/main/example_data/MicW2Graph/abundance_data_allbiomes.csv
             file_format: csv
             delimiter: ','
           - title: Abundance data for all studies (xls)
             component_type: dataframe
-            file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/example_data/MicW2Graph/1_Exploratory_Data_Analysis/1_Abundance_data/4_abundance_data_allbiomes.xls
+            file_path: example_data/MicW2Graph/1_Exploratory_Data_Analysis/1_Abundance_data/4_abundance_data_allbiomes.xls
             file_format: xls
             delimiter: ','
       - title: Sample data
         components:
           - title: Number of samples per study (png)
             component_type: plot
             plot_type: static
-            file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/example_data/MicW2Graph/1_Exploratory_Data_Analysis/2_Sample_data/3_number_samples_per_study.png
+            file_path: example_data/MicW2Graph/1_Exploratory_Data_Analysis/2_Sample_data/3_number_samples_per_study.png
           - title: Sampling countries for all studies (plotly)
             component_type: plot
             plot_type: plotly
-            file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/example_data/MicW2Graph/1_Exploratory_Data_Analysis/2_Sample_data/1_pie_plot_countries_plotly.json
+            file_path: example_data/MicW2Graph/1_Exploratory_Data_Analysis/2_Sample_data/1_pie_plot_countries_plotly.json
           - title: Sample data for all studies (parquet)
             component_type: dataframe
-            file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/example_data/MicW2Graph/1_Exploratory_Data_Analysis/2_Sample_data/4_sample_info_allbiomes.parquet
+            file_path: example_data/MicW2Graph/1_Exploratory_Data_Analysis/2_Sample_data/4_sample_info_allbiomes.parquet
             file_format: parquet
           - title: Sample data for all studies (txt)
             component_type: dataframe
-            file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/example_data/MicW2Graph/1_Exploratory_Data_Analysis/2_Sample_data/5_sample_info_allbiomes.txt
+            file_path: example_data/MicW2Graph/1_Exploratory_Data_Analysis/2_Sample_data/5_sample_info_allbiomes.txt
             file_format: txt
       - title: Extra information
         components:
@@ -66,17 +66,17 @@ sections:
           - title: Network1 (graphml)
             component_type: plot
             plot_type: interactive_network
-            file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/example_data/MicW2Graph/2_Microbial_Association_Networks/1_Network_visualization1/1_man_example.graphml
+            file_path: example_data/MicW2Graph/2_Microbial_Association_Networks/1_Network_visualization1/1_man_example.graphml
       - title: Network Visualization2
         components:
           - title: Network2 (edge list csv)
             component_type: plot
             plot_type: interactive_network
             csv_network_format: edgelist
-            file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/example_data/MicW2Graph/2_Microbial_Association_Networks/2_Network_visualization2/1_man_example.csv
+            file_path: example_data/MicW2Graph/2_Microbial_Association_Networks/2_Network_visualization2/1_man_example.csv
           - title: Edge list (csv)
             component_type: dataframe
-            file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/example_data/MicW2Graph/2_Microbial_Association_Networks/2_Network_visualization2/1_man_example.csv
+            file_path: example_data/MicW2Graph/2_Microbial_Association_Networks/2_Network_visualization2/1_man_example.csv
             file_format: csv
             delimiter: ','
             caption: This is the edge list of the network
@@ -85,13 +85,13 @@ sections:
           - title: Network3 (cyjs)
             component_type: plot
             plot_type: interactive_network
-            file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/example_data/MicW2Graph/2_Microbial_Association_Networks/3_Network_visualization3/1_man_example.cyjs
+            file_path: example_data/MicW2Graph/2_Microbial_Association_Networks/3_Network_visualization3/1_man_example.cyjs
       - title: Network Visualization4
         components:
           - title: Network4 (html)
             component_type: plot
             plot_type: interactive_network
-            file_path: /Users/asaru/Documents/DTU/MoNA/vuegen/example_data/MicW2Graph/2_Microbial_Association_Networks/4_Network_visualization4/1_ckg_network.html
+            file_path: example_data/MicW2Graph/2_Microbial_Association_Networks/4_Network_visualization4/1_ckg_network.html
       - title: Network Visualization5
         components:
           - title: Network5 (remote html)
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,10 +1,11 @@
 [tool.poetry]
-name = "report-generator"
+name = "vuegen"
 version = "0.1.0"
 description = "Module to generate automatic web interface reports with visualizations"
 authors = ["MoNA group"]
 license = "MIT"
 readme = "README.md"
+repository = "https://github.com/Multiomics-Analytics-Group/vuegen"
 
 [tool.poetry.dependencies]
 python = ">=3.9,<3.9.7 || >3.9.7,<4.0"
@@ -25,11 +26,20 @@ itables = "^2.2.2"
 kaleido = "0.2.0"
 vl-convert-python = "^1.7.0"
 dataframe-image = "^0.2.6"
-
+strenum = { version = "^0.4.15", python = "<3.11" }
 
 [tool.poetry.group.dev.dependencies]
 ipykernel = "^6.29.5"
 
+
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"
+
+# https://stackoverflow.com/a/60990574/9684872
+[tool.poetry.extras]
+streamlit = ["streamlit"]
+quarto = ["quarto", "ipykernel"]
+
+# [project.scripts]
+# my-script = "vuegen.main:main"
diff --git a/tests/test_module_imports.py b/tests/test_module_imports.py
@@ -0,0 +1,12 @@
+
+def test_imports():
+    import vuegen
+    import vuegen.main
+    import vuegen.quarto_reportview
+    import vuegen.report
+    import vuegen.report_generator
+    import vuegen.streamlit_reportview
+    import vuegen.utils
+
+    assert vuegen.__version__
+
diff --git a/vuegen/__init__.py b/vuegen/__init__.py
@@ -0,0 +1,3 @@
+from importlib.metadata import version
+
+__version__ = version("vuegen")
diff --git a/vuegen/config_manager.py b/vuegen/config_manager.py
@@ -1,8 +1,10 @@
 import os
-import report as r
 from pathlib import Path
 from typing import Dict, List, Union, Tuple
-from utils import get_logger, assert_enum_value
+
+from . import report as r
+from .utils import assert_enum_value, get_logger
+
 
 class ConfigManager:
     """
@@ -518,4 +520,4 @@ def _create_chatbot_component(self, component_data: dict) -> r.ChatBot:
             caption = component_data.get('caption'),
             headers = component_data.get('headers'),
             params = component_data.get('params')
-        )
+        )
diff --git a/vuegen/main.py b/vuegen/main.py
@@ -1,6 +1,7 @@
-import report_generator
 from pathlib import Path
-from utils import get_logger, get_args
+
+from vuegen import report_generator
+from vuegen.utils import get_args, get_logger
 
 if __name__ == '__main__':
     # Parse command-line arguments
diff --git a/vuegen/quarto_reportview.py b/vuegen/quarto_reportview.py
@@ -1,10 +1,13 @@
 import os
 import subprocess
-import report as r
 from typing import List
+
 import networkx as nx
 import pandas as pd
-from utils import create_folder, is_url
+
+from . import report as r
+from .utils import create_folder, is_url
+
 
 class QuartoReportView(r.ReportView):
     """
@@ -117,6 +120,9 @@ def run_report(self, output_dir: str = BASE_DIR) -> None:
         except subprocess.CalledProcessError as e:
             self.report.logger.error(f"Error running '{self.report.title}' {self.report_type} report: {str(e)}")
             raise
+        except FileNotFoundError as e:
+            self.report.logger.error(f"Quarto is not installed. Please install Quarto to run the report: {str(e)}")
+            raise
 
     def _create_yaml_header(self) -> str:
         """
diff --git a/vuegen/report.py b/vuegen/report.py
@@ -1,17 +1,25 @@
+import json
+import logging
 import os
 from abc import ABC, abstractmethod
 from dataclasses import dataclass, field
-from typing import ClassVar
-from enum import StrEnum, auto
-from typing import List, Optional
+from enum import auto
+
+try:
+    from enum import StrEnum
+except ImportError:
+    from strenum import StrEnum
+
+from typing import ClassVar, List, Optional
+
+import matplotlib.pyplot as plt
 import networkx as nx
 import pandas as pd
-import logging
 import requests
-import json
-import matplotlib.pyplot as plt
 from pyvis.network import Network
-from utils import cyjs_to_networkx, pyvishtml_to_networkx, fetch_file_stream
+
+from .utils import cyjs_to_networkx, fetch_file_stream, pyvishtml_to_networkx
+
 
 class ReportType(StrEnum):
     STREAMLIT = auto()
@@ -741,4 +749,4 @@ def _generate_subsection(self, subsection: Subsection) -> tuple[List[str], List[
             - list of subsection content lines (List[str])
             - list of imports for the subsection (List[str])
         """
-        pass
+        pass
diff --git a/vuegen/report_generator.py b/vuegen/report_generator.py
@@ -1,10 +1,12 @@
-from streamlit_reportview import StreamlitReportView
-from quarto_reportview import QuartoReportView
-from config_manager import ConfigManager
-from utils import assert_enum_value, load_yaml_config, write_yaml_config
-from report import ReportType
 import logging
 
+from .config_manager import ConfigManager
+from .quarto_reportview import QuartoReportView
+from .report import ReportType
+from .streamlit_reportview import StreamlitReportView
+from .utils import assert_enum_value, load_yaml_config, write_yaml_config
+
+
 def get_report(report_type: str, logger: logging.Logger, config_path: str = None, dir_path: str = None) -> None:
     """
     Generate and run a report based on the specified engine.
@@ -15,7 +17,7 @@ def get_report(report_type: str, logger: logging.Logger, config_path: str = None
         The report type. It should be one of the values of the ReportType Enum.
     logger : logging.Logger
         A logger object to track warnings, errors, and info messages.
-    config : str, optional
+    config_path : str, optional
         Path to the YAML configuration file.
     dir_path : str, optional
         Path to the directory from which to generate the configuration file.
@@ -57,4 +59,4 @@ def get_report(report_type: str, logger: logging.Logger, config_path: str = None
             report_type=report_type
         )
         quarto_report.generate_report()
-        quarto_report.run_report()
+        quarto_report.run_report()
diff --git a/vuegen/streamlit_reportview.py b/vuegen/streamlit_reportview.py
@@ -1,9 +1,12 @@
-import report as r
 import os
 import subprocess
 from typing import List
+
 import pandas as pd
-from utils import create_folder, is_url
+
+from . import report as r
+from .utils import create_folder, is_url
+
 
 class StreamlitReportView(r.WebAppReportView):
     """
@@ -659,4 +662,4 @@ def _generate_component_imports(self, component: r.Component) -> List[str]:
             component_imports.extend(components_imports['chatbot'])
 
         # Return the list of import statements
-        return component_imports     
+        return component_imports     
diff --git a/vuegen/utils.py b/vuegen/utils.py

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,3 @@`
	`1`	`+from importlib.metadata import version`
	`2`	`+`
	`3`	`+__version__ = version("vuegen")`